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Ding K, Xu Q, Zhao L, Li Y, Li Z, Shi W, Zeng Q, Wang X, Zhang X. Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis). BMC Genomics 2024; 25:373. [PMID: 38627659 PMCID: PMC11022445 DOI: 10.1186/s12864-024-10268-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb. Phylogenetically, D. delphis was close to Tursiops truncatus and T. aduncus. The genome of D. delphis exhibited 428 expanded and 1,885 contracted gene families, and 120 genes were identified as positively selected. The expansion of the HSP70 gene family suggested that D. delphis has a powerful system for buffering stress, which might be associated with its broad adaptability, longevity, and detoxification capacity. The expanded IFN-α and IFN-ω gene families, as well as the positively selected genes encoding tripartite motif-containing protein 25, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, and p38 MAP kinase, were all involved in pathways for antiviral, anti-inflammatory, and antineoplastic mechanisms. The genome data also revealed dramatic fluctuations in the effective population size during the Pleistocene. Overall, the high-quality genome assembly and annotation represent significant molecular resources for ecological and evolutionary studies of Delphinus and help support their sustainable treatment and conservation.
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Affiliation(s)
- Kui Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Liyuan Zhao
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yixuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Zhong Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Wenge Shi
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Qianhui Zeng
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xianyan Wang
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, China.
- National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology, Xi'an, China.
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2
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Foley NM, Harris AJ, Bredemeyer KR, Ruedi M, Puechmaille SJ, Teeling EC, Criscitiello MF, Murphy WJ. Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation. CELL GENOMICS 2024; 4:100482. [PMID: 38237599 PMCID: PMC10879000 DOI: 10.1016/j.xgen.2023.100482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/17/2023] [Accepted: 12/10/2023] [Indexed: 02/17/2024]
Abstract
The emergence of COVID-19 and severe acute respiratory syndrome (SARS) has prioritized understanding bats' viral tolerance. Myotis bats are exceptionally species rich and have evolved viral tolerance. They also exhibit swarming, a cryptic behavior where large, multi-species assemblages gather for mating, which has been hypothesized to promote interspecific hybridization. To resolve the coevolution of genome architecture and their unusual antiviral tolerance, we undertook a phylogenomic analysis of 60 Old World Myotis genomes. We demonstrate an extensive history of introgressive hybridization that has replaced the species phylogeny across 17%-93% of the genome except for pericentromeric regions of macrochromosomes. Introgression tracts were enriched on microchromosome regions containing key antiviral pathway genes overexpressed during viral challenge experiments. Together, these results suggest that the unusual Myotis karyotype may have evolved to selectively position immune-related genes in high recombining genomic regions prone to introgression of divergent alleles, including a diversity of interleukin loci responsible for the release of pro-inflammatory cytokines.
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Affiliation(s)
- Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Route de Malagnou 1, BP 6434, 1211 Geneva 6, Switzerland
| | - Sebastien J Puechmaille
- Institut des Sciences de l'Évolution, Montpellier (ISEM), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France; Institut Universitaire de France, Paris, France
| | - Emma C Teeling
- School of Biology and Environmental, Science, Science Centre West, University College Dublin, Belfield, Ireland
| | - Michael F Criscitiello
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA; Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA.
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3
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Pratt EAL, Beheregaray LB, Fruet P, Tezanos-Pinto G, Bilgmann K, Zanardo N, Diaz-Aguirre F, Secchi ER, Freitas TRO, Möller LM. Genomic Divergence and the Evolution of Ecotypes in Bottlenose Dolphins (Genus Tursiops). Genome Biol Evol 2023; 15:evad199. [PMID: 37935115 PMCID: PMC10655200 DOI: 10.1093/gbe/evad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 10/03/2023] [Accepted: 10/14/2023] [Indexed: 11/09/2023] Open
Abstract
Climatic changes have caused major environmental restructuring throughout the world's oceans. Marine organisms have responded to novel conditions through various biological systems, including genomic adaptation. Growing accessibility of next-generation DNA sequencing methods to study nonmodel species has recently allowed genomic changes underlying environmental adaptations to be investigated. This study used double-digest restriction-site associated DNA (ddRAD) sequence data to investigate the genomic basis of ecotype formation across currently recognized species and subspecies of bottlenose dolphins (genus Tursiops) in the Southern Hemisphere. Subspecies-level genomic divergence was confirmed between the offshore common bottlenose dolphin (T. truncatus truncatus) and the inshore Lahille's bottlenose dolphin (T. t. gephyreus) from the southwestern Atlantic Ocean (SWAO). Similarly, subspecies-level divergence is suggested between inshore (eastern Australia) Indo-Pacific bottlenose dolphin (T. aduncus) and the proposed Burrunan dolphin (T. australis) from southern Australia. Inshore bottlenose dolphin lineages generally had lower genomic diversity than offshore lineages, a pattern particularly evident for T. t. gephyreus, which showed exceptionally low diversity. Genomic regions associated with cardiovascular, musculoskeletal, and energy production systems appear to have undergone repeated adaptive evolution in inshore lineages across the Southern Hemisphere. We hypothesize that comparable selective pressures in the inshore environment drove similar adaptive responses in each lineage, supporting parallel evolution of inshore bottlenose dolphins. With climate change altering marine ecosystems worldwide, it is crucial to gain an understanding of the adaptive capacity of local species and populations. Our study provides insights into key adaptive pathways that may be important for the long-term survival of cetaceans and other organisms in a changing marine environment.
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Affiliation(s)
- Eleanor A L Pratt
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Pedro Fruet
- Laboratório de Ecologia e Conservação da Megafauna Marinha (ECOMEGA), Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Museu Oceanográfico Prof. Eliézer de C. Rios, Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Kaosa, Rio Grande, Brazil
| | | | - Kerstin Bilgmann
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Department of Environment and Water, Adelaide, South Australia, Australia
| | - Fernando Diaz-Aguirre
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Eduardo R Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha (ECOMEGA), Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Museu Oceanográfico Prof. Eliézer de C. Rios, Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
| | - Thales R O Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
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4
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Westbury MV, Cabrera AA, Rey-Iglesia A, De Cahsan B, Duchêne DA, Hartmann S, Lorenzen ED. A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea. Mol Ecol 2023; 32:4829-4843. [PMID: 37448145 DOI: 10.1111/mec.17069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/21/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
The impact of post-divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post-divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding-window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D-statistics and f-branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species' gene pools.
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Affiliation(s)
| | | | | | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - David A Duchêne
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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5
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Louis M, Korlević P, Nykänen M, Archer F, Berrow S, Brownlow A, Lorenzen ED, O'Brien J, Post K, Racimo F, Rogan E, Rosel PE, Sinding MHS, van der Es H, Wales N, Fontaine MC, Gaggiotti OE, Foote AD. Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nat Commun 2023; 14:4020. [PMID: 37463880 DOI: 10.1038/s41467-023-39532-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.
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Affiliation(s)
- Marie Louis
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK.
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark.
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
- Greenland Institute of Natural Resources, Kivioq 2, Nuuk, 3900, Greenland.
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Milaja Nykänen
- Department of Environmental and Biological Sciences, PO Box 111, FI-80101, Joensuu, Finland
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Frederick Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Eline D Lorenzen
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Joanne O'Brien
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Atlantic Technological University, Dublin Road, H91 T8NW, Galway, Ireland
| | - Klaas Post
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Fernando Racimo
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Emer Rogan
- School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork, Ireland
| | - Patricia E Rosel
- Marine Mammal and Turtle Division, Southeast Fisheries Science Center, NOAA, 646 Cajundome Boulevard, Lafayette, LA, 70506, USA
| | - Mikkel-Holger S Sinding
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Henry van der Es
- Natural History Museum Rotterdam, Westzeedijk 345, 3015 AA, Rotterdam, Netherlands
| | - Nathan Wales
- University of York, BioArCh, Environment Building, Wentworth Way, Heslington, York, YO10 5DD, UK
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
- MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) Institut de Recherche pour le Développement (IRD), F-34394, Montpellier, France
| | - Oscar E Gaggiotti
- Centre for Biological Diversity, Sir Harold Mitchell Building and Dyers Brae, University of St Andrews, St Andrews, KY16 9TH, Scotland, UK
| | - Andrew D Foote
- Department of Natural History, Norwegian University of Science and Technology (NTNU), NO-7491, Trondheim, Norway.
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316, Oslo, Norway.
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6
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Wittwer S, Gerber L, Allen SJ, Willems EP, Marfurt SM, Krützen M. Reconstructing the colonization history of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Northwestern Australia. Mol Ecol 2023. [PMID: 37173858 DOI: 10.1111/mec.16984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Bottlenose dolphins (Tursiops spp.) are found in waters around Australia, with T. truncatus typically occupying deeper, more oceanic habitat, while T. aduncus occur in shallower, coastal waters. Little is known about the colonization history of T. aduncus along the Western Australian coastline; however, it has been hypothesized that extant populations are the result of an expansion along the coastline originating from a source in the north of Australia. To investigate the history of coastal T. aduncus populations in the area, we generated a genomic SNP dataset using a double-digest restriction-site-associated DNA (ddRAD) sequencing approach. The resulting dataset consisted of 103,201 biallelic SNPs for 112 individuals which were sampled from eleven coastal and two offshore sites between Shark Bay and Cygnet Bay, Western Australia. Our population genomic analyses showed a pattern consistent with the proposed source in the north with significant isolation by distance along the coastline, as well as a reduction in genomic diversity measures along the coastline with Shark Bay showing the most pronounced reduction. Our demographic analysis indicated that the expansion of T. aduncus along the coastline began around the last glacial maximum and progressed southwards with the Shark Bay population being founded only 13 kya. Our results are in line with coastal colonization histories inferred for Tursiops globally, highlighting the ability of delphinids to rapidly colonize novel coastal niches as habitat is released during glacial cycle-related global sea level and temperature changes.
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Affiliation(s)
- Samuel Wittwer
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - Livia Gerber
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australian Capital Territory, Australia
| | - Simon J Allen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Erik P Willems
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - Svenja M Marfurt
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
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7
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Duan Y, Fu S, Ye Z, Bu W. Phylogeny of Urostylididae (Heteroptera: Pentatomoidea) reveals rapid radiation and challenges traditional classification. ZOOL SCR 2023. [DOI: 10.1111/zsc.12582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yujie Duan
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
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8
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Zhang C, Mirarab S. Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees. Mol Biol Evol 2022; 39:6750035. [PMID: 36201617 PMCID: PMC9750496 DOI: 10.1093/molbev/msac215] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 09/20/2022] [Accepted: 10/03/2022] [Indexed: 01/07/2023] Open
Abstract
Phylogenomic analyses routinely estimate species trees using methods that account for gene tree discordance. However, the most scalable species tree inference methods, which summarize independently inferred gene trees to obtain a species tree, are sensitive to hard-to-avoid errors introduced in the gene tree estimation step. This dilemma has created much debate on the merits of concatenation versus summary methods and practical obstacles to using summary methods more widely and to the exclusion of concatenation. The most successful attempt at making summary methods resilient to noisy gene trees has been contracting low support branches from the gene trees. Unfortunately, this approach requires arbitrary thresholds and poses new challenges. Here, we introduce threshold-free weighting schemes for the quartet-based species tree inference, the metric used in the popular method ASTRAL. By reducing the impact of quartets with low support or long terminal branches (or both), weighting provides stronger theoretical guarantees and better empirical performance than the unweighted ASTRAL. Our simulations show that weighting improves accuracy across many conditions and reduces the gap with concatenation in conditions with low gene tree discordance and high noise. On empirical data, weighting improves congruence with concatenation and increases support. Together, our results show that weighting, enabled by a new optimization algorithm we introduce, improves the utility of summary methods and can reduce the incongruence often observed across analytical pipelines.
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Affiliation(s)
- Chao Zhang
- Bioinformatics and Systems Biology, UC San Diego, La Jolla, CA, USA
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9
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The Seabed Makes the Dolphins: Physiographic Features Shape the Size and Structure of the Bottlenose Dolphin Geographical Units. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10081036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The common bottlenose dolphin (Tursiops truncatus) is a cosmopolitan delphinid, regularly present in the Mediterranean Sea. According to previous studies, this dolphin tends to form resident geographical units scattered on the continental shelf. We investigated how the physiographic characteristics of the area of residence, with special reference to the size and shape of the continental shelf, affect the home range and the group size of the local units. We analysed and compared data collected between 2004–2016 by 15 research groups operating in different study areas of the Mediterranean Sea: the Alboran Sea, in the South-Western Mediterranean, the Gulf of Lion and the Pelagos Sanctuary for the marine mammals, in the North-Western Mediterranean, and the Gulf of Ambracia, in the North-Central Mediterranean Sea. We have found that in areas characterised by a wide continental platform, dolphins have wider home ranges and aggregate into larger groups. In areas characterized by a narrow continental platform, dolphins show much smaller home ranges and aggregate into smaller groups. The results obtained from this collective research effort highlight the importance of data sharing to improve our scientific knowledge in the field of cetaceans and beyond.
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10
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Gómez R, Neri-Bazán RM, Posadas-Mondragon A, Vizcaíno-Dorado PA, Magaña JJ, Aguilar-Faisal JL. Molecular Assessments, Statistical Effectiveness Parameters and Genetic Structure of Captive Populations of Tursiops truncatus Using 15 STRs. Animals (Basel) 2022; 12:ani12141857. [PMID: 35883404 PMCID: PMC9312175 DOI: 10.3390/ani12141857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The bottlenose dolphins are one of the most used species in entertainment, assisted therapy, education, and research on welfare. However, their maintenance in captivity requires powerful and sensitive tools for preserving their diversity. The number of genetic markers for this purpose remains controversial, restraining the marine species’ genetic diversity determination. We aimed to select 15 hypervariable molecular markers whose statistical parameters were made in 210 captive dolphins from 18 Mexican centers to support their usefulness. The proposed set of markers allowed us to obtain a genetic fingerprint of each dolphin. Additionally, we identified the structure of the captive population, analyzing the groups according to the capture location. Such characterization is key for maintaining the captive species’ biodiversity rates within conservation and reintroduction programs. However, these 15 genetic markers can also be helpful for small- isolated populations, subspecies and other genera of endangered and vulnerable species. Abstract Genetic analysis is a conventional way of identifying and monitoring captive and wildlife species. Knowledge of statistical parameters reinforcing their usefulness and effectiveness as powerful tools for preserving diversity is crucial. Although several studies have reported the diversity of cetaceans such as Tursiops truncatus using microsatellites, its informative degree has been poorly reported. Furthermore, the genetic structure of this cetacean has not been fully studied. In the present study, we selected 15 microsatellites with which 210 dolphins were genetically characterized using capillary electrophoresis. The genetic assertiveness of this set of hypervariable markers identified one individual in the range of 6.927e13 to 1.806e16, demonstrating its substantial capability in kinship relationships. The genetic structure of these 210 dolphins was also determined regarding the putative capture origin; a genetic stratification (k = 2) was found. An additional dolphin group of undetermined origin was also characterized to challenge the proficiency of our chosen markers. The set of markers proposed herein could be a helpful tool to guarantee the maintenance of the genetic diversity rates in conservation programs both in Tursiops truncatus and across other odontocetes, Mysticeti and several genera of endangered and vulnerable species.
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Affiliation(s)
- Rocío Gómez
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | - Rocío M. Neri-Bazán
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina-Instituto Politécnico Nacional (ESM-IPN), Mexico City 11340, Mexico; (R.M.N.-B.); (A.P.-M.)
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra-Ibarra (INR-LGII), Mexico City 14389, Mexico;
| | - Araceli Posadas-Mondragon
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina-Instituto Politécnico Nacional (ESM-IPN), Mexico City 11340, Mexico; (R.M.N.-B.); (A.P.-M.)
| | - Pablo A. Vizcaíno-Dorado
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra-Ibarra (INR-LGII), Mexico City 14389, Mexico;
| | - Jonathan J. Magaña
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra-Ibarra (INR-LGII), Mexico City 14389, Mexico;
- Departamento de Bioingenieria, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey-Campus Ciudad de México (ITESM-CCM), Mexico City 14380, Mexico
- Correspondence: (J.J.M.); (J.L.A.-F.)
| | - José Leopoldo Aguilar-Faisal
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina-Instituto Politécnico Nacional (ESM-IPN), Mexico City 11340, Mexico; (R.M.N.-B.); (A.P.-M.)
- Correspondence: (J.J.M.); (J.L.A.-F.)
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11
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Faria DM, Steel D, Baker CS, da Silva JM, de Meirelles ACO, Souto LRA, Siciliano S, Barbosa LA, Secchi E, Di Tullio JC, de Oliveira LR, Ott PH, Farro APC. Mitochondrial diversity and inter-specific phylogeny among dolphins of the genus Stenella in the Southwest Atlantic Ocean. PLoS One 2022; 17:e0270690. [PMID: 35834534 PMCID: PMC9282552 DOI: 10.1371/journal.pone.0270690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
The genus Stenella is comprised of five species occurring in all oceans. Despite its wide distribution, genetic diversity information on these species is still scarce especially in the Southwest Atlantic Ocean. Some features of this genus can enhance opportunities for potential introgressive hybridization, e.g. sympatric distibution along the Brazilian coast, mixed known associations among species, karyotype uniformity and genome permeability. In this study we analyzed three genes of the mitochondrial genome to investigate the genetic diversity and occurrence of genetic mixture among eighty specimens of Stenella. All species exhibited moderate to high levels of genetic diversity (h = 0.833 to h = 1.000 and π = 0.006 to π = 0.015). Specimens of S. longirostris, S. attenuata and S. frontalis were clustered into differentiated haplogroups, in contrast, haplotypes of S. coeruleoalba and S. clymene were clustered together. We detected phylogenetic structure of mixed clades for S. clymene and S. coeruleoalba specimens, in the Southwest Atlantic Ocean, and also between S. frontalis and S. attenuata in the Northeast Atlantic Ocean, and between S. frontalis and S. longirostris in the Northwest Atlantic Ocean. These specimes were morphologically identified as one species but exhibited the maternal lineage of another species, by mitochondrial DNA. Our results demonstrate that ongoing gene flow is occurring among species of the genus Stenella reinforcing that this process could be one of the reasons for the confusing taxonomy and difficulties in elucidating phylogenetic relationships within this group.
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Affiliation(s)
- Drienne Messa Faria
- Laboratório de Genética e Conservação Animal, Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo (UFES), São Mateus, ES, Brazil
- * E-mail:
| | - Debbie Steel
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
| | - C. Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, United States of America
| | - José Martins da Silva
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Fernando de Noronha, PE, Brazil
| | | | | | - Salvatore Siciliano
- Departamento de Ciências Biológicas, Escola Nacional de Saúde Pública/Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Eduardo Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | - Juliana Couto Di Tullio
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
| | | | - Paulo Henrique Ott
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul (GEMARS), Torres, RS, Brazil
- Universidade Estadual do Rio Grande do Sul (Uergs), Osório, RS, Brazil
| | - Ana Paula Cazerta Farro
- Laboratório de Genética e Conservação Animal, Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo (UFES), São Mateus, ES, Brazil
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12
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Pratt EAL, Beheregaray LB, Bilgmann K, Zanardo N, Diaz-Aguirre F, Brauer C, Sandoval-Castillo J, Möller LM. Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity. Mol Ecol 2022; 31:2223-2241. [PMID: 35146819 DOI: 10.1111/mec.16389] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/30/2022]
Abstract
Heterogeneous seascapes and strong environmental gradients in coastal waters are expected to influence adaptive divergence, particularly in species with large population sizes where selection is expected to be highly efficient. However, these influences might also extend to species characterized by strong social structure, natal philopatry and small home ranges. We implemented a seascape genomic study to test this hypothesis in Indo-Pacific bottlenose dolphins (Tursiops aduncus) distributed along the environmentally heterogeneous coast of southern Australia. The datasets included oceanographic and environmental variables thought to be good predictors of local adaptation in dolphins and 8,081 filtered single nucleotide polymorphisms (SNPs) genotyped for individuals sampled from seven different bioregions. From a neutral perspective, population structure and connectivity of the dolphins were generally influenced by habitat type and social structuring. Genotype-environment association analysis identified 241 candidate adaptive loci and revealed that sea surface temperature and salinity gradients influenced adaptive divergence in these animals at both large- (1,000s km) and fine-scales (<100 km). Enrichment analysis and annotation of candidate genes revealed functions related to sodium-activated ion transport, kidney development, adipogenesis and thermogenesis. The findings of spatial adaptive divergence and inferences of putative physiological adaptations challenge previous suggestions that marine megafauna is most likely to be affected by environmental and climatic changes via indirect, trophic effects. Our work contributes to conservation management of coastal bottlenose dolphins subjected to anthropogenic disturbance and to efforts of clarifying how seascape heterogeneity influences adaptive diversity and evolution in small cetaceans.
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Affiliation(s)
- Eleanor A L Pratt
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Kerstin Bilgmann
- Department of Biological Sciences, Macquarie University, 2109, New South Wales, Australia
| | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Department of Environment and Water, Adelaide, 5000, South Australia, Australia
| | - Fernando Diaz-Aguirre
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Chris Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
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13
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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14
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Gray H, van Waerebeek K, Owen J, Collins T, Minton G, Ponnampalam L, Willson A, Baldwin R, Hoelzel AR. Evolutionary drivers of morphological differentiation among three bottlenose dolphin lineages, Tursiops spp. (Delphinidae), in the northwest Indian Ocean utilizing linear and geometric morphometric techniques. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Local adaptation and adaptive radiations are typically associated with phenotypic variation suited to alternative environments. In the marine environment, the nature of relevant ecological or environmental transitions is poorly understood, especially for highly mobile species. Here we compare three genetic lineages in the genus Tursiops (bottlenose dolphins), using linear measurements and geometric morphometric techniques, in the context of environmental variation in the northwest Indian Ocean. Cranial morphology was clearly differentiated comparing Tursiops truncatus and Tursiops aduncus, while a recently discovered genetic lineage, found in the Arabian Sea, was morphologically most similar to T. aduncus from the same region, but distinct for various measures, particularly metrics associated with the lateral dimension of the skull. The extent of divergence between T. truncatus and T. aduncus compared to differences between the T. aduncus lineages is consistent with the recent phylogeny for these species. Therefore, with the corroboration of genetic and morphological inference, we propose two conservation units of T. aduncus be recognized in the region at a sub-specific level so that their conservation can be managed effectively. We consider possible evolutionary mechanisms associated with regional habitat characteristics and the exploitation of distinct prey resources.
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Affiliation(s)
- Howard Gray
- Department of Biosciences, University of Durham, South Road, Durham DH1 3LE, UK
| | | | - Joseph Owen
- Department of Archaeology, Simon Fraser University, Education Building 9635, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Tim Collins
- Wildlife Conservation Society Ocean Giants Program, 2300 Southern Boulevard, Bronx, NY 10460-1099, USA
| | - Gianna Minton
- Megaptera Marine Conservation, 2242PT Den Haag, The Netherlands
| | | | - Andrew Willson
- Future Seas Global SPC, PO Box 286, Postal Code 116, Muscat, Sultanate of Oman
| | - Robert Baldwin
- Five Oceans Environmental Services, PO Box 660, PC131, Ruwi, Sultanate of Oman
| | - A Rus Hoelzel
- Department of Biosciences, University of Durham, South Road, Durham DH1 3LE, UK
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15
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Inamori D, Kita YF, Funasaka N. External Morphological and Molecular Evidence of Natural Intrageneric Hybridization between Common and Indo-Pacific Bottlenose Dolphins (Tursiops truncatus × T. aduncus) from Japanese Waters. MAMMAL STUDY 2021. [DOI: 10.3106/ms2021-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Daiki Inamori
- Taiji Whale Museum, Taiji, Higashimuro, Wakayama 649-5171, Japan
| | - Yuki F. Kita
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Minami-ku, Sapporo, Hokkaido 005-8601, Japan
| | - Noriko Funasaka
- Cetacean Research Center, Graduate School of Bioresources, Mie University, Kurimamachiya, Tsu, Mie 514-8507, Japan
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16
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Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractRecently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the genera Tursiops and Stenella are monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis of Tursiops and Stenella. Phylogenetic reconstruction with the maximum likelihood and Bayesian methods of concatenated loci, as well as with coalescence analyses of sliding window trees, produced a concordant and well-supported tree. Our studies support the non-monophyletic status of Tursiops and Stenella because the species referred these genera do not form exclusive monophyletic clades. This suggests that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity. A four-taxon D-statistic (ABBA-BABA) test, five-taxon DFOIL test, and tree-based PhyloNet analyses all showed extensive gene flow across dolphin species, which could explain the instability in resolving phylogenetic relationship of oceanic dolphins with different and limited markers. This study could be a good case to demonstrate how genomic data can reveal complex speciation and phylogeny in rapidly radiating animal groups.
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17
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Louis M, Galimberti M, Archer F, Berrow S, Brownlow A, Fallon R, Nykänen M, O'Brien J, Roberston KM, Rosel PE, Simon-Bouhet B, Wegmann D, Fontaine MC, Foote AD, Gaggiotti OE. Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. SCIENCE ADVANCES 2021; 7:eabg1245. [PMID: 34705499 PMCID: PMC8550227 DOI: 10.1126/sciadv.abg1245] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 09/08/2021] [Indexed: 05/27/2023]
Abstract
Studying repeated adaptation can provide insights into the mechanisms allowing species to adapt to novel environments. Here, we investigate repeated evolution driven by habitat specialization in the common bottlenose dolphin. Parapatric pelagic and coastal ecotypes of common bottlenose dolphins have repeatedly formed across the oceans. Analyzing whole genomes of 57 individuals, we find that ecotype evolution involved a complex reticulated evolutionary history. We find parallel linked selection acted upon ancient alleles in geographically distant coastal populations, which were present as standing genetic variation in the pelagic populations. Candidate loci evolving under parallel linked selection were found in ancient tracts, suggesting recurrent bouts of selection through time. Therefore, despite the constraints of small effective population size and long generation time on the efficacy of selection, repeated adaptation in long-lived social species can be driven by a combination of ecological opportunities and selection acting on ancestral standing genetic variation.
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Affiliation(s)
- Marie Louis
- Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews KY16 8LB, Scotland, UK
- Centre d'Etudes Biologiques de Chize, La Rochelle Université, 17000 La Rochelle, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
- Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350 Copenhagen, Denmark
| | - Marco Galimberti
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Frederick Archer
- National Marine Fisheries Service, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA
- Scripps Institution of Oceanography, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Galway-Mayo Institute of Technology, Dublin Road, H91 T8NW Galway, Ireland
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ramon Fallon
- School of Medicine, University of St Andrews, North Haugh, St Andrews, Fife KY16 9TF, Scotland, UK
| | | | - Joanne O'Brien
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Galway-Mayo Institute of Technology, Dublin Road, H91 T8NW Galway, Ireland
| | - Kelly M Roberston
- National Marine Fisheries Service, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA
| | - Patricia E Rosel
- National Marine Fisheries Service, Southeast Fisheries Science Center, NOAA, 646 Cajundome Boulevard, Lafayette, LA 70506, USA
| | - Benoit Simon-Bouhet
- Centre d'Etudes Biologiques de Chize, La Rochelle Université, 17000 La Rochelle, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES), Montpellier, France
| | - Andrew D Foote
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, UK
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim 7012, Norway
| | - Oscar E Gaggiotti
- Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews KY16 8LB, Scotland, UK
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18
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Papale EB, Azzolin MA, Cascão I, Gannier A, Lammers MO, Martin VM, Oswald JN, Perez-Gil M, Prieto R, Silva MA, Torri M, Giacoma C. Dolphin whistles can be useful tools in identifying units of conservation. BMC ZOOL 2021; 6:22. [PMID: 37170140 PMCID: PMC10127015 DOI: 10.1186/s40850-021-00085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/31/2021] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Prioritizing groupings of organisms or ‘units’ below the species level is a critical issue for conservation purposes. Several techniques encompassing different time-frames, from genetics to ecological markers, have been considered to evaluate existing biological diversity at a sufficient temporal resolution to define conservation units. Given that acoustic signals are expressions of phenotypic diversity, their analysis may provide crucial information on current differentiation patterns within species. Here, we tested whether differences previously delineated within dolphin species based on i) geographic isolation, ii) genetics regardless isolation, and iii) habitat, regardless isolation and genetics, can be detected through acoustic monitoring. Recordings collected from 104 acoustic encounters of Stenella coeruleoalba, Delphinus delphis and Tursiops truncatus in the Azores, Canary Islands, the Alboran Sea and the Western Mediterranean basin between 1996 and 2012 were analyzed. The acoustic structure of communication signals was evaluated by analyzing parameters of whistles in relation to the known genetic and habitat-driven population structure.
Results
Recordings from the Atlantic and Mediterranean were accurately assigned to their respective basins of origin through Discriminant Function Analysis, with a minimum 83.8% and a maximum 93.8% classification rate. A parallel pattern between divergence in acoustic features and in the genetic and ecological traits within the basins was highlighted through Random Forest analysis. Although it is not yet possible to establish a causal link between each driver and acoustic differences between basins, we showed that signal variation reflects fine-scale diversity and may be used as a proxy for recognizing discrete units.
Conclusion
We recommend that acoustic analysis be included in assessments of delphinid population structure, together with genetics and ecological tracer analysis. This cost-efficient non-invasive method can be applied to uncover distinctiveness and local adaptation in other wide-ranging marine species.
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19
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Vargas-Fonseca OA, Yates P, Kirkman SP, Pistorius PA, Moore DM, Natoli A, Cockcroft V, Hoelzel AR. Population structure associated with bioregion and seasonal prey distribution for Indo-Pacific bottlenose dolphins (Tursiops aduncus) in South Africa. Mol Ecol 2021; 30:4642-4659. [PMID: 34289192 DOI: 10.1111/mec.16086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/19/2021] [Accepted: 06/29/2021] [Indexed: 11/28/2022]
Abstract
Many marine species exhibit fine-scale population structure despite high mobility and a lack of physical barriers to dispersal, but the evolutionary drivers of differentiation in these systems are generally poorly understood. Here we investigate the potential role of habitat transitions and seasonal prey distributions on the evolution of population structure in the Indo-Pacific bottlenose dolphin, Tursiops aduncus, off South Africa's coast, using double-digest restriction-site associated DNA sequencing. Population structure was identified between the eastern and southern coasts and correlated with the habitat transition between the temperate Agulhas (southern) and subtropical Natal (eastern) Bioregions, suggesting differentiation driven by resource specializations. Differentiation along the Natal coast was comparatively weak, but was evident in some analyses and varied depending on whether the samples were collected during or outside the seasonal sardine (Sardinops sagax) run. This local abundance of prey could influence the ranging patterns and apparent genetic structure of T. aduncus. These findings have significant and transferable management implications, most importantly in terms of differentiating populations inhabiting distinct bioregions and seasonal structural patterns within a region associated with the movement of prey resources.
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Affiliation(s)
- O Alejandra Vargas-Fonseca
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa.,Marine Apex Predator Research Unit (MAPRU), Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South Africa
| | - Paige Yates
- Department of Biosciences, University of Durham, Durham, UK
| | - Stephan P Kirkman
- Marine Apex Predator Research Unit (MAPRU), Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South Africa.,Branch: Oceans and Coasts, Department of Environment, Forestry and Fisheries (DEFF), Cape Town, South Africa
| | - Pierre A Pistorius
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa.,Marine Apex Predator Research Unit (MAPRU), Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South Africa
| | - Daniel M Moore
- Department of Biosciences, University of Durham, Durham, UK
| | - Ada Natoli
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, United Arab Emirates.,UAE Dolphin Project, Dubai, United Arab Emirates
| | - Victor Cockcroft
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa
| | - A Rus Hoelzel
- Department of Biosciences, University of Durham, Durham, UK
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20
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Ben Chehida Y, Loughnane R, Thumloup J, Kaschner K, Garilao C, Rosel PE, Fontaine MC. No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications. Evol Appl 2021; 14:1588-1611. [PMID: 34178106 PMCID: PMC8210799 DOI: 10.1111/eva.13227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 01/12/2023] Open
Abstract
Understanding species responses to past environmental changes can help forecast how they will cope with ongoing climate changes. Harbor porpoises are widely distributed in the North Atlantic and were deeply impacted by the Pleistocene changes with the split of three subspecies. Despite major impacts of fisheries on natural populations, little is known about population connectivity and dispersal, how they reacted to the Pleistocene changes, and how they will evolve in the future. Here, we used phylogenetics, population genetics, and predictive habitat modeling to investigate population structure and phylogeographic history of the North Atlantic porpoises. A total of 925 porpoises were characterized at 10 microsatellite loci and one quarter of the mitogenome (mtDNA). A highly divergent mtDNA lineage was uncovered in one porpoise off Western Greenland, suggesting that a cryptic group may occur and could belong to a recently discovered mesopelagic ecotype off Greenland. Aside from it and the southern subspecies, spatial genetic variation showed that porpoises from both sides of the North Atlantic form a continuous system belonging to the same subspecies (Phocoena phocoena phocoena). Yet, we identified important departures from random mating and restricted dispersal forming a highly significant isolation by distance (IBD) at both mtDNA and nuclear markers. A ten times stronger IBD at mtDNA compared with nuclear loci supported previous evidence of female philopatry. Together with the lack of spatial trends in genetic diversity, this IBD suggests that migration-drift equilibrium has been reached, erasing any genetic signal of a leading-edge effect that accompanied the predicted recolonization of the northern habitats freed from Pleistocene ice. These results illuminate the processes shaping porpoise population structure and provide a framework for designing conservation strategies and forecasting future population evolution.
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Affiliation(s)
- Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Roisin Loughnane
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Julie Thumloup
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Kristin Kaschner
- Department of Biometry and Environmental System AnalysisFaculty of Environment and Natural ResourcesUniversity of FreiburgFreiburgGermany
| | | | - Patricia E. Rosel
- Southeast Fisheries Science CenterNational Marine Fisheries ServiceNOAALafayetteLAUSA
| | - Michael C. Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
- Laboratoire MIVEGEC (Université de Montpellier, CNRS, IRD)Montpellier Cedex 5France
- Centre de Recherche en Écologie et Évolution de la Santé (CREESMontpellier Cedex 5France
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21
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Batley KC, Sandoval-Castillo J, Kemper CM, Zanardo N, Tomo I, Beheregaray LB, Möller LM. Whole genomes reveal multiple candidate genes and pathways involved in the immune response of dolphins to a highly infectious virus. Mol Ecol 2021; 30:6434-6448. [PMID: 33675577 DOI: 10.1111/mec.15873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 01/02/2023]
Abstract
Wildlife species are challenged by various infectious diseases that act as important demographic drivers of populations and have become a great conservation concern particularly under growing environmental changes. The new era of whole genome sequencing provides new opportunities and avenues to explore the role of genetic variants in the plasticity of immune responses, particularly in non-model systems. Cetacean morbillivirus (CeMV) has emerged as a major viral threat to cetacean populations worldwide, contributing to the death of thousands of individuals of multiple dolphin and whale species. To understand the genomic basis of immune responses to CeMV, we generated and analysed whole genomes of 53 Indo-Pacific bottlenose dolphins (Tursiops aduncus) exposed to Australia's largest known CeMV-related mortality event that killed at least 50 dolphins from three different species. The genomic data set consisted of 10,168,981 SNPs anchored onto 23 chromosome-length scaffolds and 77 short scaffolds. Whole genome analysis indicated that levels of inbreeding in the dolphin population did not influence the outcome of an individual. Allele frequency estimates between survivors and nonsurvivors of the outbreak revealed 15,769 candidate SNPs, of which 689 were annotated to 295 protein coding genes. These included 50 genes with functions related to innate and adaptive immune responses, and cytokine signalling pathways and genes thought to be involved in immune responses to other morbilliviruses. Our study characterised genomic regions and pathways that may contribute to CeMV immune responses in dolphins. This represents a stride towards clarifying the complex interactions of the cetacean immune system and emphasises the value of whole genome data sets in understanding genetic elements that are essential for species conservation, including disease susceptibility and adaptation.
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Affiliation(s)
- Kimberley C Batley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,Cetacean Ecology, Behaviour, and Evolution Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | | | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,Cetacean Ecology, Behaviour, and Evolution Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Ikuko Tomo
- South Australian Museum, Adelaide, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.,Cetacean Ecology, Behaviour, and Evolution Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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22
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Brookwell R, Finlayson K, van de Merwe JP. A comparative analysis of the karyotypes of three dolphins - Tursiops truncatus Montagu, 1821, Tursiops australis Charlton-Robb et al., 2011, and Grampus griseus Cuvier, 1812. COMPARATIVE CYTOGENETICS 2021; 15:53-63. [PMID: 33628396 PMCID: PMC7892529 DOI: 10.3897/compcytogen.v15.i1.60398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
The aim of this study is to produce G-banded karyotypes of three dolphin species, Tursiops truncatus Montagu, 1821, Tursiops australisCharlton-Robb et al., 2011, and Grampus griseus Cuvier, 1812, and to determine if any differences between the species can be observed. Monolayer skin cultures were established and processed for chromosome study by trypsin banding. The results indicate that the three species here investigated have the same diploid number (2n = 44) and very similar gross chromosome morphology, however G-banding allows distinction between each species. Chromosome 1 in G. griseus is significantly different from the other 2 species, and chromosome 2 in T. australis is subtly different from the other 2 species. This result is of potential significance in taxonomic studies, and can provide an unequivocal answer in the assessment of suspected hybrids between these species.
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Affiliation(s)
- Ross Brookwell
- Cytogenetics Department, Sullivan Nicolaides Pathology, 24 Hurworth street, Bowen Hills, Queensland, 4006, AustraliaCytogenetics Department, Sullivan Nicolaides PathologyBowen HillsAustralia
| | - Kimberly Finlayson
- Australian Rivers Institute, Griffith University Gold Coast, Edmund Rice drive, Southport, Queensland, 4215, AustraliaGriffith University Gold CoastSouthportAustralia
| | - Jason P. van de Merwe
- Australian Rivers Institute, Griffith University Gold Coast, Edmund Rice drive, Southport, Queensland, 4215, AustraliaGriffith University Gold CoastSouthportAustralia
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23
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Uckele KA, Adams RP, Schwarzbach AE, Parchman TL. Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny. Mol Phylogenet Evol 2020; 156:107022. [PMID: 33242585 DOI: 10.1016/j.ympev.2020.107022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 10/06/2020] [Accepted: 11/17/2020] [Indexed: 12/22/2022]
Abstract
Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin clade, as well as a number of close and distant relatives, to improve understanding of diversification in this group. Phylogenetic analyses using three methods (SVDquartets, maximum likelihood, and Bayesian) yielded highly congruent and well-resolved topologies. These phylogenies provided improved resolution relative to past analyses based on Sanger sequencing of nuclear and chloroplast DNA, and were largely consistent with taxonomic expectations based on geography and morphology. Calibration of a Bayesian phylogeny with fossil evidence produced divergence time estimates for the clade consistent with a late Oligocene origin in North America, followed by a period of elevated diversification between 12 and 5 Mya. Comparison of the ddRADseq phylogenies with a phylogeny based on Sanger-sequenced chloroplast DNA revealed five instances of pronounced discordance, illustrating the potential for chloroplast introgression, chloroplast transfer, or incomplete lineage sorting to influence organellar phylogeny. Our results improve understanding of the pattern and tempo of diversification in Juniperus, and highlight the utility of reduced-representation sequencing for resolving phylogenetic relationships in non-model organisms with reticulation and recent divergence.
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Affiliation(s)
- Kathryn A Uckele
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
| | - Robert P Adams
- Baylor University, Utah Lab, 201 N 5500 W, Hurricane, UT 84790, USA.
| | - Andrea E Schwarzbach
- Department of Health and Biomedical Sciences, University of Texas - Rio Grande Valley, 1 W University Drive, Brownsville, TX 78520, USA.
| | - Thomas L Parchman
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
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24
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Duchen P, Salamin N. A Cautionary Note on the Use of Genotype Callers in Phylogenomics. Syst Biol 2020; 70:844-854. [PMID: 33084875 PMCID: PMC8208803 DOI: 10.1093/sysbio/syaa081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Next-generation-sequencing genotype callers are commonly used in studies to call variants from newly sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However, when these callers are used at the phylogenetic level, the consequences for downstream analyses can be substantial. Here, we performed simulations to compare the performance between the genotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show that the genotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also found that the accuracy of heterozygote calls declines with increasing distance to the reference genome. We quantified this decline and found that it is very sharp in GATK, while ATLAS maintains high accuracy even at moderately divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies. [ATLAS; efficiency of SNP calling; GATK; heterozygote calling; next-generation sequencing; reference genome; variant calling.]
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Affiliation(s)
- Pablo Duchen
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
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25
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Ben Chehida Y, Thumloup J, Schumacher C, Harkins T, Aguilar A, Borrell A, Ferreira M, Rojas-Bracho L, Robertson KM, Taylor BL, Víkingsson GA, Weyna A, Romiguier J, Morin PA, Fontaine MC. Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum. Sci Rep 2020; 10:15190. [PMID: 32938978 PMCID: PMC7494866 DOI: 10.1038/s41598-020-71603-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/17/2020] [Indexed: 01/30/2023] Open
Abstract
Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.
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Affiliation(s)
- Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Julie Thumloup
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Cassie Schumacher
- Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI, 48103, USA
| | - Timothy Harkins
- Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI, 48103, USA
| | - Alex Aguilar
- IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, 08071, Barcelona, Spain
| | - Asunción Borrell
- IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, 08071, Barcelona, Spain
| | - Marisa Ferreira
- MATB-Sociedade Portuguesa de Vida Selvagem, Estação de Campo de Quiaios, Apartado EC Quiaios, 3080-530, Figueira da Foz, Portugal.,CPRAM-Ecomare, Estrada Do Porto de Pesca Costeira, 3830-565, Gafanha da Nazaré, Portugal
| | - Lorenzo Rojas-Bracho
- Comisión Nacional de Áreas Naturales Protegidas (CONANP), C/o Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, BC, Mexico
| | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Gísli A Víkingsson
- Marine and Freshwater Research Institute, Fornubúðum 5, 220, Hafnarfjörður, Iceland
| | - Arthur Weyna
- Institut Des Sciences de L'Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France
| | - Jonathan Romiguier
- Institut Des Sciences de L'Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands. .,Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) et Centre de Recherche en Écologie et Évolution de la Santé (CREES), Institut de Recherche Pour Le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France.
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